7D5W

Bovine heart cytochrome c oxidase in a catalytic intermediate of O at 1.84 angstrom resolution

  • Classification: OXIDOREDUCTASE
  • Organism(s): Bos taurus
  • Mutation(s): No 

  • Deposited: 2020-09-28 Released: 2021-07-21 
  • Deposition Author(s): Tsukihara, T., Shimada, A.
  • Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Critical roles of the Cu B site in efficient proton pumping as revealed by crystal structures of mammalian cytochrome c oxidase catalytic intermediates.

Shimada, A.Hara, F.Shinzawa-Itoh, K.Kanehisa, N.Yamashita, E.Muramoto, K.Tsukihara, T.Yoshikawa, S.

(2021) J Biol Chem 297: 100967-100967

  • DOI: https://doi.org/10.1016/j.jbc.2021.100967
  • Primary Citation of Related Structures:  
    7CP5, 7D5W, 7D5X

  • PubMed Abstract: 

    Mammalian cytochrome c oxidase (CcO) reduces O 2 to water in a bimetallic site including Fe a3 and Cu B giving intermediate molecules, termed A-, P-, F-, O-, E-, and R-forms. From the P-form on, each reaction step is driven by single-electron donations from cytochrome c coupled with the pumping of a single proton through the H-pathway, a proton-conducting pathway composed of a hydrogen-bond network and a water channel. The proton-gradient formed is utilized for ATP production by F-ATPase. For elucidation of the proton pumping mechanism, crystal structural determination of these intermediate forms is necessary. Here we report X-ray crystallographic analysis at ∼1.8 Å resolution of fully reduced CcO crystals treated with O 2 for three different time periods. Our disentanglement of intermediate forms from crystals that were composed of multiple forms determined that these three crystallographic data sets contained ∼45% of the O-form structure, ∼45% of the E-form structure, and ∼20% of an oxymyoglobin-type structure consistent with the A-form, respectively. The O- and E-forms exhibit an unusually long Cu B 2+ -OH - distance and Cu B 1+ -H 2 O structure keeping Fe a3 3+ -OH - state, respectively, suggesting that the O- and E-forms have high electron affinities that cause the O→E and E→R transitions to be essentially irreversible and thus enable tightly coupled proton pumping. The water channel of the H-pathway is closed in the O- and E-forms and partially open in the R-form. These structures, together with those of the recently reported P- and F-forms, indicate that closure of the H-pathway water channel avoids back-leaking of protons for facilitating the effective proton pumping.


  • Organizational Affiliation

    Picobiology Institute, Graduate School of Life Science, University of Hyogo, kamigori, Akoh, Hyogo, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1
A, N
514Bos taurusMutation(s): 0 
EC: 7.1.1.9
UniProt
Find proteins for P00396 (Bos taurus)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2
B, O
227Bos taurusMutation(s): 0 
EC: 7.1.1.9
UniProt
Find proteins for P68530 (Bos taurus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3
C, P
259Bos taurusMutation(s): 0 
EC: 7.1.1.9
UniProt
Find proteins for P00415 (Bos taurus)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
D, Q
144Bos taurusMutation(s): 0 
UniProt
Find proteins for P00423 (Bos taurus)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrial
E, R
105Bos taurusMutation(s): 0 
UniProt
Find proteins for P00426 (Bos taurus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B, mitochondrial
F, S
94Bos taurusMutation(s): 0 
UniProt
Find proteins for P00428 (Bos taurus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2, mitochondrial
G, T
84Bos taurusMutation(s): 0 
UniProt
Find proteins for P07471 (Bos taurus)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1
H, U
79Bos taurusMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6C
I, V
73Bos taurusMutation(s): 0 
UniProt
Find proteins for P04038 (Bos taurus)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A1, mitochondrial
J, W
58Bos taurusMutation(s): 0 
UniProt
Find proteins for P07470 (Bos taurus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7B, mitochondrial
K, X
49Bos taurusMutation(s): 0 
UniProt
Find proteins for P13183 (Bos taurus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrial
L, Y
46Bos taurusMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8B, mitochondrial
M, Z
43Bos taurusMutation(s): 0 
UniProt
Find proteins for P10175 (Bos taurus)
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Small Molecules
Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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KB [auth C],
KD [auth N],
NF [auth T],
SE [auth P]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
TGL
Query on TGL

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DD [auth L]
FA [auth A]
GA [auth A]
QD [auth N]
RD [auth N]
DD [auth L],
FA [auth A],
GA [auth A],
QD [auth N],
RD [auth N],
SD [auth N]
TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
HEA
Query on HEA

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AA [auth A],
BA [auth A],
LD [auth N],
MD [auth N]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PEK
Query on PEK

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FB [auth C]
GB [auth C]
HB [auth C]
MF [auth T]
OE [auth P]
FB [auth C],
GB [auth C],
HB [auth C],
MF [auth T],
OE [auth P],
PE [auth P]
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE
C43 H78 N O8 P
ANRKEHNWXKCXDB-BHFWLYLHSA-N
PSC
Query on PSC

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HE [auth O],
JA [auth A]
(7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE
C42 H81 N O8 P
JLPULHDHAOZNQI-AUSZDXHESA-O
PGV
Query on PGV

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HA [auth A]
IB [auth C]
JB [auth C]
KA [auth A]
QE [auth P]
HA [auth A],
IB [auth C],
JB [auth C],
KA [auth A],
QE [auth P],
RE [auth P],
TD [auth N],
VD [auth N]
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
DMU
Query on DMU

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AD [auth K]
AG [auth Z]
BD [auth K]
BF [auth P]
CD [auth K]
AD [auth K],
AG [auth Z],
BD [auth K],
BF [auth P],
CD [auth K],
CF [auth P],
DC [auth D],
DF [auth Q],
EC [auth D],
HD [auth L],
ID [auth M],
LE [auth O],
MB [auth C],
TE [auth P],
UF [auth X],
VF [auth X],
WA [auth A],
WF [auth X],
XB [auth C],
XC [auth J],
XF [auth X],
YC [auth K],
ZC [auth K]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
CHD
Query on CHD

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DB [auth C]
ED [auth L]
LB [auth C]
ME [auth P]
RC [auth G]
DB [auth C],
ED [auth L],
LB [auth C],
ME [auth P],
RC [auth G],
UC [auth J],
YA [auth B],
ZF [auth Y]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
CUA
Query on CUA

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GE [auth O],
XA [auth B]
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
PO4
Query on PO4

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RF [auth U],
TC [auth H]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
Query on ZN

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FF [auth S],
IC [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU

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CA [auth A],
ND [auth N]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO
Query on EDO

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AB [auth B]
AC [auth D]
AE [auth N]
AF [auth P]
BB [auth B]
AB [auth B],
AC [auth D],
AE [auth N],
AF [auth P],
BB [auth B],
BC [auth D],
BE [auth N],
CB [auth B],
CC [auth D],
CE [auth N],
DE [auth N],
EE [auth N],
EF [auth Q],
FC [auth E],
FD [auth L],
FE [auth N],
GC [auth E],
GD [auth L],
GF [auth S],
HC [auth E],
HF [auth S],
IE [auth O],
IF [auth S],
JC [auth F],
JD [auth M],
JE [auth O],
JF [auth S],
KC [auth F],
KE [auth O],
KF [auth S],
LA [auth A],
LC [auth F],
LF [auth S],
MA [auth A],
MC [auth F],
NA [auth A],
NB [auth C],
NC [auth F],
OA [auth A],
OB [auth C],
OC [auth F],
OF [auth T],
PA [auth A],
PB [auth C],
PC [auth F],
PF [auth T],
QA [auth A],
QB [auth C],
QC [auth F],
QF [auth T],
RA [auth A],
RB [auth C],
SA [auth A],
SB [auth C],
SC [auth G],
SF [auth W],
TA [auth A],
TB [auth C],
TF [auth W],
UA [auth A],
UB [auth C],
UE [auth P],
VA [auth A],
VB [auth C],
VC [auth J],
VE [auth P],
WB [auth C],
WC [auth J],
WD [auth N],
WE [auth P],
XD [auth N],
XE [auth P],
YB [auth D],
YD [auth N],
YE [auth P],
YF [auth Y],
ZA [auth B],
ZB [auth D],
ZD [auth N],
ZE [auth P]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
PER
Query on PER

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IA [auth A],
UD [auth N]
PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N
MG
Query on MG

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DA [auth A],
OD [auth N]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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EA [auth A],
EB [auth C],
NE [auth P],
PD [auth N]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A, N
L-PEPTIDE LINKINGC6 H11 N O3 SMET
SAC
Query on SAC
I, V
L-PEPTIDE LINKINGC5 H9 N O4SER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.435α = 90
b = 203.092β = 90
c = 177.794γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
HKL-2000data scaling
DMphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanKAKENHI Grants 18K06092
Japan Society for the Promotion of Science (JSPS)JapanKAKENHI Grants 15K18493
Japan Science and TechnologyJapanCREST 12101577

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-21
    Type: Initial release
  • Version 1.1: 2021-08-04
    Changes: Database references
  • Version 1.2: 2021-09-15
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description